Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Knowledge Representation Standards and Interchange Formats for Causal Graphs

In many domains, automated reasoning tools must represent graphs of causally linked events. These include fault-tree analysis, probabilistic risk assessment (PRA), planning, procedures, medical reasoning about disease progression, and functional architectures. Each of these fields has its own requirements for the representation of causation, events, actors and conditions. The representations include ontologies of function and cause, data dictionaries for causal dependency, failure and hazard, and interchange formats between some existing tools. In none of the domains has a generally accepted interchange format emerged. The paper makes progress towards interoperability across the wide range of causal analysis methodologies. We survey existing practice and emerging interchange formats in each of these fields. Setting forth a set of terms and concepts that are broadly shared across the domains, we examine the several ways in which current practice represents them. Some phenomena are difficult to represent or to analyze in several domains. These include mode transitions, reachability analysis, positive and negative feedback loops, conditions correlated but not causally linked and bimodal probability distributions. We work through examples and contrast the differing methods for addressing them. We detail recent work in knowledge interchange formats for causal trees in aerospace analysis applications in early design, safety and reliability. Several examples are discussed, with a particular focus on reachability analysis and mode transitions. We generalize the aerospace analysis work across the several other domains. We also recommend features and capabilities for the next generation of causal knowledge representation standards

A Data Model for Exploration of Temporal Virtual Reality Geographic Information Systems

Geographic information systems deal with the exploration, analysis, and presentation of geo-referenced data. Virtual reality is a type of human-computer interface that comes close to the way people perceive information in the real world. Thus, virtual reality environments become the natural paradigm for extending and enhancing the presentational and exploratory capability of GIs applications in both the spatial and temporal domains. The main motivation of this thesis is the lack of a framework that properly supports the exploration of geographic information in a multi-dimensional and multi-sensorial environment (i.e., temporal virtual reality geographic information systems). This thesis introduces a model for virtual exploration of animations. Virtual exploration of animations is a framework composed of abstract data types and a user interface that allow non-expert users to control, manipulate, analyze, and present objects\u27 behaviors in a virtual-reality environment. In the model for virtual exploration of animations, the manipulation of the dynamic environment is accomplished through a set of operations performed over abstractions that represent temporal characteristics of actions. An important feature of the model is that the temporal information is treated as first-class entities and not as a mere attribute of action\u27s representations. Therefore, entities of the temporal model have their own built-in functionality and are able to represent complex temporal structures. In an environment designed for the manipulation of the temporal characteristics of actions, the knowledge of relationships among objects\u27 behaviors plays a significant role in the model. This information comes from the knowledge base of the application domain and is represented in the model through constraints among entities of the temporal model. Such constraints vary from simply relating the end points of two intervals to a complex mechanism that takes into account all relations between sequences of intervals of cyclic behaviors. The fact that the exploration of the information takes place in a virtual reality environment imposes new requirements on the animation model. This thesis introduces a new classification of objects in a VR environment and describes the associated semantics of each element in the taxonomy. These semantics are used to direct the way an object interacts with an observer and with other objects in the environment

Cognitive Modeling for Computer Animation: A Comparative Review

Cognitive modeling is a provocative new paradigm that paves the way towards intelligent graphical characters by providing them with logic and reasoning skills. Cognitively empowered self-animating characters will see in the near future a widespread use in the interactive game, multimedia, virtual reality and production animation industries. This review covers three recently-published papers from the field of cognitive modeling for computer animation. The approaches and techniques employed are very different. The cognition model in the first paper is built on top of Soar, which is intended as a general cognitive architecture for developing systems that exhibit intelligent behaviors. The second paper uses an active plan tree and a plan library to achieve the fast and robust reactivity to the environment changes. The third paper, based on an AI formalism known as the situation calculus, develops a cognitive modeling language called CML and uses it to specify a behavior outline or sketch plan to direct the characters in terms of goals. Instead of presenting each paper in isolation then comparatively analyzing them, we take a top-down approach by first classifying the field into three different categories and then attempting to put each paper into a proper category. Hopefully in this way it can provide a more cohesive, systematic view of cognitive modeling approaches employed in computer animation

CLiFF Notes: Research In Natural Language Processing at the University of Pennsylvania

The Computational Linguistics Feedback Forum (CLIFF) is a group of students and faculty who gather once a week to discuss the members\u27 current research. As the word feedback suggests, the group\u27s purpose is the sharing of ideas. The group also promotes interdisciplinary contacts between researchers who share an interest in Cognitive Science. There is no single theme describing the research in Natural Language Processing at Penn. There is work done in CCG, Tree adjoining grammars, intonation, statistical methods, plan inference, instruction understanding, incremental interpretation, language acquisition, syntactic parsing, causal reasoning, free word order languages, ... and many other areas. With this in mind, rather than trying to summarize the varied work currently underway here at Penn, we suggest reading the following abstracts to see how the students and faculty themselves describe their work. Their abstracts illustrate the diversity of interests among the researchers, explain the areas of common interest, and describe some very interesting work in Cognitive Science. This report is a collection of abstracts from both faculty and graduate students in Computer Science, Psychology and Linguistics. We pride ourselves on the close working relations between these groups, as we believe that the communication among the different departments and the ongoing inter-departmental research not only improves the quality of our work, but makes much of that work possible

CLiFF Notes: Research in the Language, Information and Computation Laboratory of the University of Pennsylvania

One concern of the Computer Graphics Research Lab is in simulating human task behavior and understanding why the visualization of the appearance, capabilities and performance of humans is so challenging. Our research has produced a system, called Jack, for the definition, manipulation, animation and human factors analysis of simulated human figures. Jack permits the envisionment of human motion by interactive specification and simultaneous execution of multiple constraints, and is sensitive to such issues as body shape and size, linkage, and plausible motions. Enhanced control is provided by natural behaviors such as looking, reaching, balancing, lifting, stepping, walking, grasping, and so on. Although intended for highly interactive applications, Jack is a foundation for other research. The very ubiquitousness of other people in our lives poses a tantalizing challenge to the computational modeler: people are at once the most common object around us, and yet the most structurally complex. Their everyday movements are amazingly fluid, yet demanding to reproduce, with actions driven not just mechanically by muscles and bones but also cognitively by beliefs and intentions. Our motor systems manage to learn how to make us move without leaving us the burden or pleasure of knowing how we did it. Likewise we learn how to describe the actions and behaviors of others without consciously struggling with the processes of perception, recognition, and language. Present technology lets us approach human appearance and motion through computer graphics modeling and three dimensional animation, but there is considerable distance to go before purely synthesized figures trick our senses. We seek to build computational models of human like figures which manifest animacy and convincing behavior. Towards this end, we: Create an interactive computer graphics human model; Endow it with reasonable biomechanical properties; Provide it with human like behaviors; Use this simulated figure as an agent to effect changes in its world; Describe and guide its tasks through natural language instructions. There are presently no perfect solutions to any of these problems; ultimately, however, we should be able to give our surrogate human directions that, in conjunction with suitable symbolic reasoning processes, make it appear to behave in a natural, appropriate, and intelligent fashion. Compromises will be essential, due to limits in computation, throughput of display hardware, and demands of real-time interaction, but our algorithms aim to balance the physical device constraints with carefully crafted models, general solutions, and thoughtful organization. The Jack software is built on Silicon Graphics Iris 4D workstations because those systems have 3-D graphics features that greatly aid the process of interacting with highly articulated figures such as the human body. Of course, graphics capabilities themselves do not make a usable system. Our research has therefore focused on software to make the manipulation of a simulated human figure easy for a rather specific user population: human factors design engineers or ergonomics analysts involved in visualizing and assessing human motor performance, fit, reach, view, and other physical tasks in a workplace environment. The software also happens to be quite usable by others, including graduate students and animators. The point, however, is that program design has tried to take into account a wide variety of physical problem oriented tasks, rather than just offer a computer graphics and animation tool for the already computer sophisticated or skilled animator. As an alternative to interactive specification, a simulation system allows a convenient temporal and spatial parallel programming language for behaviors. The Graphics Lab is working with the Natural Language Group to explore the possibility of using natural language instructions, such as those found in assembly or maintenance manuals, to drive the behavior of our animated human agents. (See the CLiFF note entry for the AnimNL group for details.) Even though Jack is under continual development, it has nonetheless already proved to be a substantial computational tool in analyzing human abilities in physical workplaces. It is being applied to actual problems involving space vehicle inhabitants, helicopter pilots, maintenance technicians, foot soldiers, and tractor drivers. This broad range of applications is precisely the target we intended to reach. The general capabilities embedded in Jack attempt to mirror certain aspects of human performance, rather than the specific requirements of the corresponding workplace. We view the Jack system as the basis of a virtual animated agent that can carry out tasks and instructions in a simulated 3D environment. While we have not yet fooled anyone into believing that the Jack figure is real , its behaviors are becoming more reasonable and its repertoire of actions more extensive. When interactive control becomes more labor intensive than natural language instructional control, we will have reached a significant milestone toward an intelligent agent

Research in the Language, Information and Computation Laboratory of the University of Pennsylvania

This report takes its name from the Computational Linguistics Feedback Forum (CLiFF), an informal discussion group for students and faculty. However the scope of the research covered in this report is broader than the title might suggest; this is the yearly report of the LINC Lab, the Language, Information and Computation Laboratory of the University of Pennsylvania. It may at first be hard to see the threads that bind together the work presented here, work by faculty, graduate students and postdocs in the Computer Science and Linguistics Departments, and the Institute for Research in Cognitive Science. It includes prototypical Natural Language fields such as: Combinatorial Categorial Grammars, Tree Adjoining Grammars, syntactic parsing and the syntax-semantics interface; but it extends to statistical methods, plan inference, instruction understanding, intonation, causal reasoning, free word order languages, geometric reasoning, medical informatics, connectionism, and language acquisition. Naturally, this introduction cannot spell out all the connections between these abstracts; we invite you to explore them on your own. In fact, with this issue it’s easier than ever to do so: this document is accessible on the “information superhighway”. Just call up http://www.cis.upenn.edu/~cliff-group/94/cliffnotes.html In addition, you can find many of the papers referenced in the CLiFF Notes on the net. Most can be obtained by following links from the authors’ abstracts in the web version of this report. The abstracts describe the researchers’ many areas of investigation, explain their shared concerns, and present some interesting work in Cognitive Science. We hope its new online format makes the CLiFF Notes a more useful and interesting guide to Computational Linguistics activity at Penn